Print functions and back-tick markup for AlignIO page etc

See #47.

Author: peterjc

wiki/AlignIO.md

@@ -6,15 +6,15 @@ tags:
  - Wiki Documentation
 ---
 
-This page describes Bio.AlignIO, a new multiple sequence Alignment
+This page describes `Bio.AlignIO`, a new multiple sequence Alignment
 Input/Output interface for BioPython 1.46 and later.
 
 In addition to the built in API documentation, there is a whole chapter
 in the [Tutorial](http://biopython.org/DIST/docs/tutorial/Tutorial.html)
 on Bio.AlignIO, and although there is some overlap it is well worth
-reading in addition to this WIKI page. There is also the [API
+reading in addition to this page. There is also the [API
 documentation](http://biopython.org/DIST/docs/api/Bio.AlignIO-module.html)
-(which you can read online, or from within Python with the help
+(which you can read online, or from within Python with the `help()`
 command).
 
 Aims
@@ -23,21 +23,21 @@ Aims
 You may already be familiar with the [Bio.SeqIO](SeqIO "wikilink")
 module which deals with files containing one or more sequences
 represented as [SeqRecord](SeqRecord "wikilink") objects. The purpose of
-the SeqIO module is to provide a simple uniform interface to assorted
+the `SeqIO` module is to provide a simple uniform interface to assorted
 sequence file formats.
 
-Similarly, Bio.AlignIO deals with files containing one or more sequence
-alignments represented as Alignment objects. Bio.AlignIO uses the same
-set of functions for input and output as in Bio.SeqIO, and the same
+Similarly, `Bio.AlignIO` deals with files containing one or more sequence
+alignments represented as Alignment objects. `Bio.AlignIO` uses the same
+set of functions for input and output as in `Bio.SeqIO`, and the same
 names for the file formats supported.
 
-Note that the inclusion of Bio.AlignIO does lead to some duplication or
-choice in how to deal with some file formats. For example, Bio.AlignIO
-and Bio.Nexus will both read alignments from NEXUS files - but Bio.NEXUS
-allows more control and the use of trees.
+Note that the inclusion of `Bio.AlignIO` does lead to some duplication or
+choice in how to deal with some file formats. For example, `Bio.AlignIO`
+and `Bio.Nexus` will both read alignments from NEXUS files - but
+`Bio.NEXUS` allows more control and the use of trees.
 
 My vision is that for reading or writing sequence alignments you should
-try Bio.AlignIO as your first choice. In some cases you may only care
+try `Bio.AlignIO` as your first choice. In some cases you may only care
 about the sequences themselves, in which case try using
 [Bio.SeqIO](SeqIO "wikilink") on the alignment file directly. Unless you
 have some very specific requirements, I hope this should suffice.
@@ -98,48 +98,50 @@ Fib\_gamma](http://pfam.sanger.ac.uk/family?acc=PF09395). At the time of
 writing, this contained 14 sequences with an alignment length of 77
 amino acids, and is shown below in the PFAM or Stockholm format:
 
-    # STOCKHOLM 1.0
-    #=GS Q7ZVG7_BRARE/37-110  AC Q7ZVG7.1
-    #=GS Q6X871_SCAAQ/1-77    AC Q6X871.1
-    #=GS O02676_CROCR/1-77    AC O02676.1
-    #=GS Q6X869_TENEC/1-77    AC Q6X869.1
-    #=GS FIBG_HUMAN/40-116    AC P02679.3
-    #=GS O02689_TAPIN/1-77    AC O02689.1
-    #=GS O02688_PIG/1-77      AC O02688.1
-    #=GS O02672_9CETA/1-77    AC O02672.1
-    #=GS O02682_EQUPR/1-77    AC O02682.1
-    #=GS Q6X870_CYNVO/1-77    AC Q6X870.1
-    #=GS FIBG_RAT/40-116      AC P02680.3
-    #=GS Q6X866_DROAU/1-76    AC Q6X866.1
-    #=GS O93568_CHICK/40-116  AC O93568.1
-    #=GS FIBG_XENLA/38-114    AC P17634.1
-    Q7ZVG7_BRARE/37-110          GFGTYCPTTCGVADYLQRYKPDMDKKLDDMEQDLEEIANLTRGAQDKVVYLK---DSEAQAQKQSPDTYIKKSSNML
-    Q6X871_SCAAQ/1-77            RFGSYCPTTCGIADFLSTYQATVDKDLQTLEDILSQAENKTMEAKELVKAIQVSYLPEDPARPNRVELATKDSKKMM
-    O02676_CROCR/1-77            RFGSYCPTTCGIADFLSTYQTGVXNDLRTLEDLLSGIENKTSEAKELIKSIQVSYNPNEPPKPNTIVSATKDSKKMM
-    Q6X869_TENEC/1-77            RFGSYCPTTCGIADFLSTYQGSIDKDLQTLEDILNQVENKTXEASELIKSIQVSYNPDEPPRPNMIEGATQKSKKML
-    FIBG_HUMAN/40-116            RFGSYCPTTCGIADFLSTYQTKVDKDLQSLEDILHQVENKTSEVKQLIKAIQLTYNPDESSKPNMIDAATLKSRKML
-    #=GS FIBG_HUMAN/40-116    DR PDB; 1qvh L;14-45
-    #=GS FIBG_HUMAN/40-116    DR PDB; 1fza C;88-90
-    #=GS FIBG_HUMAN/40-116    DR PDB; 1fzb C;88-90
-    #=GS FIBG_HUMAN/40-116    DR PDB; 1fzb F;88-90
-    #=GS FIBG_HUMAN/40-116    DR PDB; 1qvh I;14-45
-    #=GS FIBG_HUMAN/40-116    DR PDB; 1fza F;88-90
-    #=GR FIBG_HUMAN/40-116    SS CCXCXBXXHHHHHHHHHHHHHHHHHHHHHHHXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX-CC
-    O02689_TAPIN/1-77            RFGSYCPTTCGIADFLSTYQTXVDKDLQVLEDILNQAENKTSEAKELIKAIQVRYKPDEPTKPGGIDSATRESKKML
-    O02688_PIG/1-77              RFGSYCPTMCGIAGFLSTYQNTVEKDLQNLEGILHQVENKTSEARELIKAIQISYNPEDLSKPDRIQSATKESKKML
-    O02672_9CETA/1-77            RFGSYCPTTCGVADFLSNYQTSVDKDLQNLEGILYQVENKTSEARELVKAIQISYNPDEPSKPNNIESATKNSKRMM
-    O02682_EQUPR/1-77            RFGSYCPTTCGIADFLSNYQTSVDKDLQDFEDILHRAENQTSEAEQLIQAIRTSYNPDEPPKTGRIDAATRESKKMM
-    Q6X870_CYNVO/1-77            RFGSYCPTTCGIADFLSTYQTKVDEDLQNLEDILYRVENRTSEAKELIKAIQVDYNPGEPPKQSVTEGATQNAKKMV
-    FIBG_RAT/40-116              RFGSYCPTTCGISDFLNSYQTDVDTDLQTLENILQRAENRTTEAKELIKAIQVYYNPDQPPKPGMIEGATQKSKKMV
-    Q6X866_DROAU/1-76            RFGSYCPTTCGIADFLNKYQTTIDQDLRHMEETLRDIDNKTAESTLLIQKIQIGQTPDPRPQ-NVIGDVTQKSRKMI
-    O93568_CHICK/40-116          RFGSYCPTTCGIADFFNKYRLTTDGELLEIEGLLQQATNSTGSIEYLIQHIKTIYPSEKQTLPQSIEQLTQKSKKII
-    #=GS O93568_CHICK/40-116  DR PDB; 1m1j F;14-90
-    #=GS O93568_CHICK/40-116  DR PDB; 1m1j C;14-90
-    #=GR O93568_CHICK/40-116  SS CCEEEEE-CCCCCCCCCCCCCHHHCCCCCHHHHHHHHHHHHHHHCCCCCCHHHHS-SSTT--SS-HHHHHHHHHHHH
-    FIBG_XENLA/38-114            RFGEYCPTTCGISDFLNRYQENVDTDLQYLENLLTQISNSTSGTTIIVEHLIDSGKKPATSPQTAIDPMTQKSKTCW
-    #=GC SS_cons                 CCECEEE-CCCCCCCCCCCCCHHHCCCCCHHHHHHHHHHHHHHHCCCCCCHHHHS-SSTT--SS-HHHHHHHHHHCC
-    #=GC seq_cons                RFGSYCPTTCGIADFLSsYQssVDcDLQsLEsILpplEN+ToEAc-LIKuIQlsYsP--ss+PstI-uATpcSKKMl
-    //
+```
+# STOCKHOLM 1.0
+#=GS Q7ZVG7_BRARE/37-110  AC Q7ZVG7.1
+#=GS Q6X871_SCAAQ/1-77    AC Q6X871.1
+#=GS O02676_CROCR/1-77    AC O02676.1
+#=GS Q6X869_TENEC/1-77    AC Q6X869.1
+#=GS FIBG_HUMAN/40-116    AC P02679.3
+#=GS O02689_TAPIN/1-77    AC O02689.1
+#=GS O02688_PIG/1-77      AC O02688.1
+#=GS O02672_9CETA/1-77    AC O02672.1
+#=GS O02682_EQUPR/1-77    AC O02682.1
+#=GS Q6X870_CYNVO/1-77    AC Q6X870.1
+#=GS FIBG_RAT/40-116      AC P02680.3
+#=GS Q6X866_DROAU/1-76    AC Q6X866.1
+#=GS O93568_CHICK/40-116  AC O93568.1
+#=GS FIBG_XENLA/38-114    AC P17634.1
+Q7ZVG7_BRARE/37-110          GFGTYCPTTCGVADYLQRYKPDMDKKLDDMEQDLEEIANLTRGAQDKVVYLK---DSEAQAQKQSPDTYIKKSSNML
+Q6X871_SCAAQ/1-77            RFGSYCPTTCGIADFLSTYQATVDKDLQTLEDILSQAENKTMEAKELVKAIQVSYLPEDPARPNRVELATKDSKKMM
+O02676_CROCR/1-77            RFGSYCPTTCGIADFLSTYQTGVXNDLRTLEDLLSGIENKTSEAKELIKSIQVSYNPNEPPKPNTIVSATKDSKKMM
+Q6X869_TENEC/1-77            RFGSYCPTTCGIADFLSTYQGSIDKDLQTLEDILNQVENKTXEASELIKSIQVSYNPDEPPRPNMIEGATQKSKKML
+FIBG_HUMAN/40-116            RFGSYCPTTCGIADFLSTYQTKVDKDLQSLEDILHQVENKTSEVKQLIKAIQLTYNPDESSKPNMIDAATLKSRKML
+#=GS FIBG_HUMAN/40-116    DR PDB; 1qvh L;14-45
+#=GS FIBG_HUMAN/40-116    DR PDB; 1fza C;88-90
+#=GS FIBG_HUMAN/40-116    DR PDB; 1fzb C;88-90
+#=GS FIBG_HUMAN/40-116    DR PDB; 1fzb F;88-90
+#=GS FIBG_HUMAN/40-116    DR PDB; 1qvh I;14-45
+#=GS FIBG_HUMAN/40-116    DR PDB; 1fza F;88-90
+#=GR FIBG_HUMAN/40-116    SS CCXCXBXXHHHHHHHHHHHHHHHHHHHHHHHXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX-CC
+O02689_TAPIN/1-77            RFGSYCPTTCGIADFLSTYQTXVDKDLQVLEDILNQAENKTSEAKELIKAIQVRYKPDEPTKPGGIDSATRESKKML
+O02688_PIG/1-77              RFGSYCPTMCGIAGFLSTYQNTVEKDLQNLEGILHQVENKTSEARELIKAIQISYNPEDLSKPDRIQSATKESKKML
+O02672_9CETA/1-77            RFGSYCPTTCGVADFLSNYQTSVDKDLQNLEGILYQVENKTSEARELVKAIQISYNPDEPSKPNNIESATKNSKRMM
+O02682_EQUPR/1-77            RFGSYCPTTCGIADFLSNYQTSVDKDLQDFEDILHRAENQTSEAEQLIQAIRTSYNPDEPPKTGRIDAATRESKKMM
+Q6X870_CYNVO/1-77            RFGSYCPTTCGIADFLSTYQTKVDEDLQNLEDILYRVENRTSEAKELIKAIQVDYNPGEPPKQSVTEGATQNAKKMV
+FIBG_RAT/40-116              RFGSYCPTTCGISDFLNSYQTDVDTDLQTLENILQRAENRTTEAKELIKAIQVYYNPDQPPKPGMIEGATQKSKKMV
+Q6X866_DROAU/1-76            RFGSYCPTTCGIADFLNKYQTTIDQDLRHMEETLRDIDNKTAESTLLIQKIQIGQTPDPRPQ-NVIGDVTQKSRKMI
+O93568_CHICK/40-116          RFGSYCPTTCGIADFFNKYRLTTDGELLEIEGLLQQATNSTGSIEYLIQHIKTIYPSEKQTLPQSIEQLTQKSKKII
+#=GS O93568_CHICK/40-116  DR PDB; 1m1j F;14-90
+#=GS O93568_CHICK/40-116  DR PDB; 1m1j C;14-90
+#=GR O93568_CHICK/40-116  SS CCEEEEE-CCCCCCCCCCCCCHHHCCCCCHHHHHHHHHHHHHHHCCCCCCHHHHS-SSTT--SS-HHHHHHHHHHHH
+FIBG_XENLA/38-114            RFGEYCPTTCGISDFLNRYQENVDTDLQYLENLLTQISNSTSGTTIIVEHLIDSGKKPATSPQTAIDPMTQKSKTCW
+#=GC SS_cons                 CCECEEE-CCCCCCCCCCCCCHHHCCCCCHHHHHHHHHHHHHHHCCCCCCHHHHS-SSTT--SS-HHHHHHHHHHCC
+#=GC seq_cons                RFGSYCPTTCGIADFLSsYQssVDcDLQsLEsILpplEN+ToEAc-LIKuIQlsYsP--ss+PstI-uATpcSKKMl
+//
+```
 
 You will notice that there is plenty of annotation information here,
 including accession numbers for each sequence and also some PDB database
@@ -149,53 +151,54 @@ chick fibrinogen proteins.
 This file contains a single alignment, so we can use the
 `Bio.AlignIO.read()` function to load it in Biopython. Let's assume
 you have downloaded this alignment from Sanger, or have copy and pasted
-the text above, and saved this as a file called `PF09395\_seed.sth` on
+the text above, and saved this as a file called `PF09395_seed.sth` on
 your computer. Then in python:
 
 ``` python
 from Bio import AlignIO
 alignment = AlignIO.read(open("PF09395_seed.sth"), "stockholm")
-print "Alignment length %i" % alignment.get_alignment_length()
+print("Alignment length %i" % alignment.get_alignment_length())
 for record in alignment :
-    print record.seq, record.id
+    print(record.seq + " " + record.id)
 ```
 
 That should give:
 
-    Alignment length 77
-    GFGTYCPTTCGVADYLQRYKPDMDKKLDDMEQDLEEIANLTRGAQDKVVYLK---DSEAQAQKQSPDTYIKKSSNML Q7ZVG7_BRARE/37-110
-    RFGSYCPTTCGIADFLSTYQATVDKDLQTLEDILSQAENKTMEAKELVKAIQVSYLPEDPARPNRVELATKDSKKMM Q6X871_SCAAQ/1-77
-    RFGSYCPTTCGIADFLSTYQTGVXNDLRTLEDLLSGIENKTSEAKELIKSIQVSYNPNEPPKPNTIVSATKDSKKMM O02676_CROCR/1-77
-    RFGSYCPTTCGIADFLSTYQGSIDKDLQTLEDILNQVENKTXEASELIKSIQVSYNPDEPPRPNMIEGATQKSKKML Q6X869_TENEC/1-77
-    RFGSYCPTTCGIADFLSTYQTKVDKDLQSLEDILHQVENKTSEVKQLIKAIQLTYNPDESSKPNMIDAATLKSRKML FIBG_HUMAN/40-116
-    RFGSYCPTTCGIADFLSTYQTXVDKDLQVLEDILNQAENKTSEAKELIKAIQVRYKPDEPTKPGGIDSATRESKKML O02689_TAPIN/1-77
-    RFGSYCPTMCGIAGFLSTYQNTVEKDLQNLEGILHQVENKTSEARELIKAIQISYNPEDLSKPDRIQSATKESKKML O02688_PIG/1-77
-    RFGSYCPTTCGVADFLSNYQTSVDKDLQNLEGILYQVENKTSEARELVKAIQISYNPDEPSKPNNIESATKNSKRMM O02672_9CETA/1-77
-    RFGSYCPTTCGIADFLSNYQTSVDKDLQDFEDILHRAENQTSEAEQLIQAIRTSYNPDEPPKTGRIDAATRESKKMM O02682_EQUPR/1-77
-    RFGSYCPTTCGIADFLSTYQTKVDEDLQNLEDILYRVENRTSEAKELIKAIQVDYNPGEPPKQSVTEGATQNAKKMV Q6X870_CYNVO/1-77
-    RFGSYCPTTCGISDFLNSYQTDVDTDLQTLENILQRAENRTTEAKELIKAIQVYYNPDQPPKPGMIEGATQKSKKMV FIBG_RAT/40-116
-    RFGSYCPTTCGIADFLNKYQTTIDQDLRHMEETLRDIDNKTAESTLLIQKIQIGQTPDPRPQ-NVIGDVTQKSRKMI Q6X866_DROAU/1-76
-    RFGSYCPTTCGIADFFNKYRLTTDGELLEIEGLLQQATNSTGSIEYLIQHIKTIYPSEKQTLPQSIEQLTQKSKKII O93568_CHICK/40-116
-    RFGEYCPTTCGISDFLNRYQENVDTDLQYLENLLTQISNSTSGTTIIVEHLIDSGKKPATSPQTAIDPMTQKSKTCW FIBG_XENLA/38-114
+```
+Alignment length 77
+GFGTYCPTTCGVADYLQRYKPDMDKKLDDMEQDLEEIANLTRGAQDKVVYLK---DSEAQAQKQSPDTYIKKSSNML Q7ZVG7_BRARE/37-110
+RFGSYCPTTCGIADFLSTYQATVDKDLQTLEDILSQAENKTMEAKELVKAIQVSYLPEDPARPNRVELATKDSKKMM Q6X871_SCAAQ/1-77
+RFGSYCPTTCGIADFLSTYQTGVXNDLRTLEDLLSGIENKTSEAKELIKSIQVSYNPNEPPKPNTIVSATKDSKKMM O02676_CROCR/1-77
+RFGSYCPTTCGIADFLSTYQGSIDKDLQTLEDILNQVENKTXEASELIKSIQVSYNPDEPPRPNMIEGATQKSKKML Q6X869_TENEC/1-77
+RFGSYCPTTCGIADFLSTYQTKVDKDLQSLEDILHQVENKTSEVKQLIKAIQLTYNPDESSKPNMIDAATLKSRKML FIBG_HUMAN/40-116
+RFGSYCPTTCGIADFLSTYQTXVDKDLQVLEDILNQAENKTSEAKELIKAIQVRYKPDEPTKPGGIDSATRESKKML O02689_TAPIN/1-77
+RFGSYCPTMCGIAGFLSTYQNTVEKDLQNLEGILHQVENKTSEARELIKAIQISYNPEDLSKPDRIQSATKESKKML O02688_PIG/1-77
+RFGSYCPTTCGVADFLSNYQTSVDKDLQNLEGILYQVENKTSEARELVKAIQISYNPDEPSKPNNIESATKNSKRMM O02672_9CETA/1-77
+RFGSYCPTTCGIADFLSNYQTSVDKDLQDFEDILHRAENQTSEAEQLIQAIRTSYNPDEPPKTGRIDAATRESKKMM O02682_EQUPR/1-77
+RFGSYCPTTCGIADFLSTYQTKVDEDLQNLEDILYRVENRTSEAKELIKAIQVDYNPGEPPKQSVTEGATQNAKKMV Q6X870_CYNVO/1-77
+RFGSYCPTTCGISDFLNSYQTDVDTDLQTLENILQRAENRTTEAKELIKAIQVYYNPDQPPKPGMIEGATQKSKKMV FIBG_RAT/40-116
+RFGSYCPTTCGIADFLNKYQTTIDQDLRHMEETLRDIDNKTAESTLLIQKIQIGQTPDPRPQ-NVIGDVTQKSRKMI Q6X866_DROAU/1-76
+RFGSYCPTTCGIADFFNKYRLTTDGELLEIEGLLQQATNSTGSIEYLIQHIKTIYPSEKQTLPQSIEQLTQKSKKII O93568_CHICK/40-116
+RFGEYCPTTCGISDFLNRYQENVDTDLQYLENLLTQISNSTSGTTIIVEHLIDSGKKPATSPQTAIDPMTQKSKTCW FIBG_XENLA/38-114
+```
 
 Alignment Output
 ----------------
 
 As in [Bio.SeqIO](SeqIO "wikilink"), there is a single output function
-**Bio.AlignIO.write()**. This takes three arguments: some alignments, a
+`Bio.AlignIO.write()`. This takes three arguments: some alignments, a
 file handle to write to, and the format to use.
 
-As of Biopython 1.48, the alignment object acquired a **format()**
+As of Biopython 1.48, the alignment object acquired a `.format()`
 method to give a string containing the alignment in the specified file
 format, e.g.
 
 ``` python
 AlignIO.read(open("PF09395_seed.sth"), "stockholm")
-print alignment.format("fasta")
+print(alignment.format("fasta"))
 ```
 
-This wiki section needs to be filled out, so in the short term please
-refer to the Bio.AlignIO chapter in the Tutorial.
+Please refer to the Bio.AlignIO chapter in the Tutorial for more details.
 
 File Format Conversion
 ----------------------