|
1 | | -Summary: |
2 | | - pullseq: extract sequences from a fasta/fastq file. This program is |
| 1 | +This software includes two applications: pullseq and seqdiff. |
| 2 | + |
| 3 | +Pullseq Summary: |
| 4 | + pullseq - extract sequences from a fasta/fastq file. This program is |
3 | 5 | fast, and can be useful in a variety of situations. You can use it to |
4 | 6 | extract sequences from one fasta/fastq file into a new file, given |
5 | 7 | either a list of header ids to include / exclude or a size minimum / |
@@ -34,22 +36,56 @@ Synopsis: |
34 | 36 | -v, --verbose, Print extra details during the run |
35 | 37 | --version, Output version information and exit |
36 | 38 |
|
| 39 | + |
| 40 | +Seqdiff Summary: |
| 41 | + seqdiff - compare two fasta (or fastq) files to determine overlap of |
| 42 | + sequences. This overlap can be at the sequence level (are two |
| 43 | + sequences exactly the same in both files?) or at the header name |
| 44 | + level (do two sequences contain the same header name between the two |
| 45 | + files?). |
| 46 | + |
| 47 | +Synopsis: |
| 48 | + seqdiff -1 first_file.fa -2 second_file.fa |
| 49 | + |
| 50 | +Usage: |
| 51 | + seqdiff -1 <first input fasta/fastq file> -2 <second fasta/fastq file> |
| 52 | + |
| 53 | + Options: |
| 54 | + -1, --first, First sequence file (required) |
| 55 | + -2, --second, Second sequence file (required) |
| 56 | + -a, --a_output, File name for uniques from first file |
| 57 | + -b, --b_output, File name for uniques from second file |
| 58 | + -c, --c_output, File name for common entries |
| 59 | + -d, --headers, Compare headers instead of sequences (default: false) |
| 60 | + -s, --summary, Just show summary stats? (default: false) |
| 61 | + -h, --help, Display this help and exit |
| 62 | + -v, --verbose, Print extra details during the run |
| 63 | + --version, Output version information and exit |
| 64 | + |
37 | 65 | REQUIREMENTS: |
38 | | - Pullseq requires a C compiler and has been tested to work with |
39 | | - either GCC or clang. Pullseq also requires and includes kseq.h |
40 | | - (Heng Li). |
| 66 | + Pullseq/Seqdiff require a C compiler and has been tested to work with |
| 67 | + either GCC or clang. They also require (and include) kseq.h (Heng |
| 68 | + Li) and uthash.h (http://troydhanson.github.com/uthash/). |
41 | 69 |
|
42 | | - Pullseq (actually kseq.h) also requires Zlib (so your linker |
43 | | - should be able to handle the '-lz' option). You can obtain zlib |
44 | | - from http://www.zlib.net/ or commonly from your OS package manager |
45 | | - (e.g. apt-get zlib or emerge zlib). |
| 70 | + kseq.h also requires Zlib (so your linker should be able to handle |
| 71 | + the '-lz' option). You can obtain zlib from http://www.zlib.net/ |
| 72 | + or commonly from your OS package manager (e.g. apt-get zlib or |
| 73 | + emerge zlib). |
46 | 74 |
|
47 | 75 | INSTALL: |
48 | | - To install pullseq, do the following in a shell on your system... |
| 76 | + To install, do the following in a shell on your system... |
49 | 77 |
|
| 78 | + From Git: |
50 | 79 | git clone https://github.com/bcthomas/pullseq.git # checkout the code using git |
51 | 80 | cd pullseq |
52 | 81 | ./bootstrap # get set up for config/build after cloning |
53 | 82 | ./configure # configure the application based on your system |
54 | 83 | make # will build the application |
55 | 84 | make install # will install in /usr/local by default |
| 85 | + |
| 86 | + From a Tar file: |
| 87 | + tar xvf pullseq_version.tar.gz |
| 88 | + cd pullseq_version |
| 89 | + ./configure # configure the application based on your system |
| 90 | + make # will build the application |
| 91 | + make install # will install in /usr/local by default |
0 commit comments