In [1]:

cd /Volumes/Bay3/Software

/Volumes/Bay3/Software

In [3]:

cd ncbi-blast-2.2.27+/bin/

/Volumes/Bay3/Software/ncbi-blast-2.2.27+/bin

In [4]:

ls

blast_formatter*   blastn*            deltablast*        makembindex*       rpstblastn*        update_blastdb.pl*
blastdb_aliastool* blastp*            dustmasker*        makeprofiledb*     segmasker*         windowmasker*
blastdbcheck*      blastx*            legacy_blast.pl*   psiblast*          tblastn*
blastdbcmd*        convert2blastmask* makeblastdb*       rpsblast*          tblastx*

In [5]:

./blastn

  File "<ipython-input-5-0561265429af>", line 1
    ./blastn
    ^
SyntaxError: invalid syntax

In [6]:

run blastn

  File "/Volumes/Bay3/Software/ncbi-blast-2.2.27+/bin/blastn", line 1
SyntaxError: Non-ASCII character '\xca' in file /Volumes/Bay3/Software/ncbi-blast-2.2.27+/bin/blastn on line 1, but no encoding declared; see http://www.python.org/peps/pep-0263.html for details

In [8]:

!blastn

/bin/sh: blastn: command not found

In [9]:

cd ..

/Volumes/Bay3/Software/ncbi-blast-2.2.27+

In [10]:

ls

ChangeLog*         LICENSE*           README*            bin/               doc/               ncbi_package_info*

In [11]:

cd bin

/Volumes/Bay3/Software/ncbi-blast-2.2.27+/bin

In [12]:

ls

blast_formatter*   blastn*            deltablast*        makembindex*       rpstblastn*        update_blastdb.pl*
blastdb_aliastool* blastp*            dustmasker*        makeprofiledb*     segmasker*         windowmasker*
blastdbcheck*      blastx*            legacy_blast.pl*   psiblast*          tblastn*
blastdbcmd*        convert2blastmask* makeblastdb*       rpsblast*          tblastx*

In [13]:

!blastn

/bin/sh: blastn: command not found

In [14]:

cd ..

/Volumes/Bay3/Software/ncbi-blast-2.2.27+

In [15]:

cd ..

/Volumes/Bay3/Software

In [16]:

cd ncbi-blast-2.2.26+/

/Volumes/Bay3/Software/ncbi-blast-2.2.26+

In [17]:

ls

ChangeLog          README             blastdb.ncbirc     doc/               out/
LICENSE            bin/               db/                ncbi_package_info  query/

In [23]:

cd ..

/Volumes/Bay3/Software/ncbi-blast-2.2.26+

In [24]:

cd ..

/Volumes/Bay3/Software

In [25]:

cp ncbi-blast-2.2.27+/bin/* /usr/local/bin

In [27]:

!blastn

BLAST query/options error: Either a BLAST database or subject sequence(s) must be specified

In [28]:

!makeblasdb

/bin/sh: makeblasdb: command not found

In [29]:

!makeblastdb

USAGE
  makeblastdb [-h] [-help] [-in input_file] [-input_type type]
    -dbtype molecule_type [-title database_title] [-parse_seqids]
    [-hash_index] [-mask_data mask_data_files] [-gi_mask]
    [-gi_mask_name gi_based_mask_names] [-out database_name]
    [-max_file_sz number_of_bytes] [-taxid TaxID] [-taxid_map TaxIDMapFile]
    [-logfile File_Name] [-version]

DESCRIPTION
   Application to create BLAST databases, version 2.2.27+

Use '-help' to print detailed descriptions of command line arguments
========================================================================

Error: Argument "dbtype". Mandatory value is missing:  `String, `nucl', `prot''

In [33]:

!makeblastdb -in /Users/sr320/Desktop/QPX_transcriptome_v1.fasta -dbtype nucl -out /Volumes/Bay3/Software/ncbi-blast-2.2.27\+/db/QPX_tran_v1plos


Building a new DB, current time: 05/02/2013 13:56:40
New DB name:   /Volumes/Bay3/Software/ncbi-blast-2.2.27+/db/QPX_tran_v1plos
New DB title:  /Users/sr320/Desktop/QPX_transcriptome_v1.fasta
Sequence type: Nucleotide
Keep Linkouts: T
Keep MBits: T
Maximum file size: 1000000000B
Adding sequences from FASTA; added 11271 sequences in 0.944333 seconds.

In [34]:

!makeblastdb -in /Users/sr320/Desktop/QPX_v015.fasta -dbtype nucl -out /Volumes/Bay3/Software/ncbi-blast-2.2.27\+/db/QPX_v015


Building a new DB, current time: 05/02/2013 13:59:27
New DB name:   /Volumes/Bay3/Software/ncbi-blast-2.2.27+/db/QPX_v015
New DB title:  /Users/sr320/Desktop/QPX_v015.fasta
Sequence type: Nucleotide
Keep Linkouts: T
Keep MBits: T
Maximum file size: 1000000000B
Adding sequences from FASTA; added 21280 sequences in 1.99526 seconds.

In [35]:

!blastn -query /Users/sr320/Desktop/QPX_transcriptome_v1.fasta -db /Volumes/Bay3/Software/ncbi-blast-2.2.27\+/db/QPX_v015 -out /Volumes/web/cnidarian/QPX_trans_blastn_genome -outfmt 6 -evalue 1E-5 -max_target_seqs 1 -num_threads 2 -task blastn

In [43]:

head /Volumes/web/cnidarian/QPX_trans_blastn_genome

---------------------------------------------------------------------------
NameError                                 Traceback (most recent call last)
<ipython-input-43-b84294e9129a> in <module>()
----> 1 head /Volumes/web/cnidarian/QPX_trans_blastn_genome

NameError: name 'head' is not defined

In [44]:

!head /Volumes/web/cnidarian/QPX_trans_blastn_genome

QPX_transcriptome_v1_Contig_1	QPX_v015_contig_5139	100.00	1269	0	0	246	1514	2166	898	0.0	2289
QPX_transcriptome_v1_Contig_2	QPX_v015_contig_1360	100.00	3682	0	0	1	3682	3900	7581	0.0	6641
QPX_transcriptome_v1_Contig_3	QPX_v015_contig_3723	99.79	2337	5	0	1	2337	2886	550	0.0	4192
QPX_transcriptome_v1_Contig_4	QPX_v015_contig_4109	99.82	1110	2	0	7	1116	1862	753	0.0	1994
QPX_transcriptome_v1_Contig_6	QPX_v015_contig_10488	99.12	913	8	0	1	913	915	3	0.0	1611
QPX_transcriptome_v1_Contig_7	QPX_v015_contig_1558	100.00	564	0	0	1	564	3588	3025	0.0	1018
QPX_transcriptome_v1_Contig_8	QPX_v015_contig_3052	100.00	2228	0	0	1	2228	3651	1424	0.0	4019
QPX_transcriptome_v1_Contig_9	QPX_v015_contig_4909	100.00	1971	0	0	1	1971	6230	8200	0.0	3555
QPX_transcriptome_v1_Contig_10	QPX_v015_contig_4102	100.00	1862	0	0	1	1862	2453	592	0.0	3359
QPX_transcriptome_v1_Contig_11	QPX_v015_contig_2947	99.48	1530	8	0	986	2515	1751	222	0.0	2724

In [ ]: