xyaneon/sequence-aligner

Performs semi-global alignments on FASTA sequences. Homework 3 for Dr. Miller's Intro to Bioinformatics class.

sequence-aligner's Issues

Meet Homework 3 requirements

Basically, it's page 56 of our class textbook, Putting Your Skills into Practice, part 5.

First letters of sequences not showing in alignments

There must be an off-by-one error somewhere...

Nicely display longer alignments over multiple lines

From the class notes website:

For extra credit on Homework Assignment 3, add numbers to make longer alignments more readable something like this:

$ ruby semi-global.rb acalifornia2009.fasta acalifornia2009m1.fasta
Alignment 1
Sequence 1 0001 TAGATATTAAAGATGAGTCTTCTAACCGAGGTCGAAACGTACGTTCTTTCTATCATCCCG
                            ||||||||||||||||||||||||||||||||||||||||||||||||
Sequence 2 0001 ____________ATGAGTCTTCTAACCGAGGTCGAAACGTACGTTCTTTCTATCATCCCG

Sequence 1 0061 TCAGGCCCCCTCAAAGCCGAGATCGCGCAGAGACTGGAAAGTGTCTTTGCAGGAAAGAAC
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sequence 2 0049 TCAGGCCCCCTCAAAGCCGAGATCGCGCAGAGACTGGAAAGTGTCTTTGCAGGAAAGAAC

Sequence 1 0121 ACAGATCTTGAGGCTCTCATGGAATGGCTAAAGACAAGACCAATCTTGTCACCTCTGACT
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sequence 2 0109 ACAGATCTTGAGGCTCTCATGGAATGGCTAAAGACAAGACCAATCTTGTCACCTCTGACT

Sequence 1 0181 AAGGGAATTTTAGGATTTGTGTTCACGCTCACCGTGCCCAGTGAGCGAGGACTGCAGCGT
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sequence 2 0169 AAGGGAATTTTAGGATTTGTGTTCACGCTCACCGTGCCCAGTGAGCGAGGACTGCAGCGT

Sequence 1 0241 AGACGCTTTGTCCAAAATGCCCTAAATGGGAATGGGGACCCGAACAACATGGATAGAGCA
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sequence 2 0229 AGACGCTTTGTCCAAAATGCCCTAAATGGGAATGGGGACCCGAACAACATGGATAGAGCA

Sequence 1 0301 GTTAAACTATACAAGAAGCTCAAAAGAGAAATAACGTTCCATGGGGCCAAGGAGGTGTCA
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sequence 2 0289 GTTAAACTATACAAGAAGCTCAAAAGAGAAATAACGTTCCATGGGGCCAAGGAGGTGTCA

Sequence 1 0361 CTAAGCTATTCAACTGGTGCACTTGCCAGTTGCATGGGCCTCATATACAACAGGATGGGA
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sequence 2 0349 CTAAGCTATTCAACTGGTGCACTTGCCAGTTGCATGGGCCTCATATACAACAGGATGGGA

Sequence 1 0421 ACAGTGACCACAGAAGCTGCTTTTGGTCTAGTGTGTGCCACTTGTGAACAGATTGCTGAT
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sequence 2 0409 ACAGTGACCACAGAAGCTGCTTTTGGTCTAGTGTGTGCCACTTGTGAACAGATTGCTGAT

Sequence 1 0481 TCACAGCATCGGTCTCACAGACAGATGGCTACTACCACCAATCCACTAATCAGGCATGAA
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sequence 2 0469 TCACAGCATCGGTCTCACAGACAGATGGCTACTACCACCAATCCACTAATCAGGCATGAA

Sequence 1 0541 AACAGAATGGTGCTGGCTAGCACTACGGCAAAGGCTATGGAACAGATGGCTGGATCGAGT
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sequence 2 0529 AACAGAATGGTGCTGGCTAGCACTACGGCAAAGGCTATGGAACAGATGGCTGGATCGAGT

Sequence 1 0601 GAACAGGCAGCGGAGGCCATGGAGGTTGCTAATCAGACTAGGCAGATGGTACATGCAATG
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sequence 2 0589 GAACAGGCAGCGGAGGCCATGGAGGTTGCTAATCAGACTAGGCAGATGGTACATGCAATG

Sequence 1 0661 AGAACTATTGGGACTCATCCTAGCTCCAGTGCTGGTCTGAAAGATGACCTTCTTGAAAAT
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sequence 2 0649 AGAACTATTGGGACTCATCCTAGCTCCAGTGCTGGTCTGAAAGATGACCTTCTTGAAAAT

Sequence 1 0721 TTGCAGGCCTACCAGAAGCGAATGGGAGTGCAGATGCAGCGATTCAAGTGATCCTCTCGT
                |||||||||||||||||||||||||||||||||||||||||||||||||||         
Sequence 2 0709 TTGCAGGCCTACCAGAAGCGAATGGGAGTGCAGATGCAGCGATTCAAGTGA_________

Sequence 1 0781 CATTGCAGCAAATATCATTGGGATCTTGCACCTGATATTGTGGATTACTGATCGTCTTTT

Sequence 2 0760 ____________________________________________________________

Sequence 1 0841 TTTCAAATGTATTTATCGTCGCTTTAAATACGGTTTGAAAAGAGGGCCTTCTACGGAAGG

Sequence 2 0760 ____________________________________________________________

Sequence 1 0901 AGTGCCTGAGTCCATGAGGGAAGAATATCAACAGGAACAGCAGAGTGCTGTGGATGTTGA

Sequence 2 0760 ____________________________________________________________

Sequence 1 0961 CGATGGTCATTTTGTCAACATAGAGCTAGAGTAAAAAACTAC

Sequence 2 0760 __________________________________________

Make terminal output of dynamic programming table nicer

Currently, we get yucky misaligned cells like this:

Dynamic programming table:
 |  | C| A| C| G| T| A| T|
-+--+--+--+--+--+--+--+--+
 |  |  |  |  |  |  |  |  |
 | 0|<-1|<-2| -3| -4| -5| -6|<-7|
-+--+--+--+--+--+--+--+--+
 |  |\ |  |\ |  |  |  |  |
C| -1| 1|<0|<-1| -2| -3| -4|<-5|
-+--+--+--+--+--+--+--+--+
 |  |  |\ |  |\ |  |  |  |
G| -2| 0| 1| 0| 0|<-1| -2|<-3|
-+--+--+--+--+--+--+--+--+
 |  |  |  |\ |  |\ |\ |\ |
C| -3| -1| 0| 2|<1|<0|<-1|<-2|
-+--+--+--+--+--+--+--+--+
 | ^| ^|\ | ^|\ |\ |\ |  |
A| -4| -2| 0| 1| 2|<1| 1|<0|
-+--+--+--+--+--+--+--+--+

Add page print support to HTML output

Perhaps this would be useful?

Backlinks on bottom and right edges not being properly cleaned up

These were supposed to be cleaned up as well, but they're still there for whatever reason.